So, I would think this may be a unique need, but I also want the same thing in Photoshop and Flash, so I figured I'd ask here.
I'd like to be able to assign layers to a Tag or Category in order to group them for management without changing the order.
For example, I have a series of layers that I want for the final product, but are resource intensive (lots of features, blend modes, etc.), so I don't always need them on. So I can turn them on and off individually, or by selecting them all and then ctrl + clicking the box, but it'd be far more efficient if I could group them (e.g. "Laggy Layers") so I could turn them all on or off at once.

Being able to add these to a category or thematic group (Highlight effects, Cartographic cheating, etc.) so they could be managed as one unit while maintaining layer order would be an amazing addition and help a lot.